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smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis
https://bioconductor.org/packages/GWASTools
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Enabling parallel processing and faster processing of intensity files #3

Closed DanielEWeeks closed 4 years ago

DanielEWeeks commented 5 years ago

Here I made changes to let 'allow.fork' to be toggled on/off in several functions, including the GdsGenotypeReader and GdsReader and gdsSubset functions. This lets us run some slower processes in parallel.

And I sped up anomDetectLOH by changing it to use the faster bind_rows function from the tidyverse package instead of the slower rbind.

(I also altered the wording in the GWASTools-package.Rd so I could tell whether I had the forked version installed or not - you would not want to import that wording change, but I wasn't sure how to exclude it from the pull request).

Thanks, Dan Weeks

smgogarten commented 4 years ago

Thanks! The forking is excellent and was requested by another user (https://github.com/zhengxwen/gdsfmt/issues/26)

I'm going to change import(tidyverse) to importFrom(dplyr, bind_rows). tidyverse has a lot of dependencies.